This study examined the use of chloroquine (CQ) to modulate autophagy flux in the brains of wild-type (WT) and Huntington's disease (HD) mice. CQ levels were measured in the brain, muscle, and blood of WT mice up to 24 hours after injection. CQ treatment resulted in variable changes to autophagy markers like LC3II and p62 across brain regions and tissue preparations. HD mice exposed to CQ had diminished levels of LC3II, p62, and LAMP-2A, with increased levels of RAB7. Higher levels of mutant huntingtin were found in the membrane fraction of CQ-treated HD mouse brains. The findings suggest that